Align deoxynucleoside transporter, permease component 1 (characterized)
to candidate GFF4163 PS417_21325 arabinose ABC transporter permease
Query= reanno::Burk376:H281DRAFT_01115 (357 letters) >FitnessBrowser__WCS417:GFF4163 Length = 321 Score = 138 bits (347), Expect = 2e-37 Identities = 93/303 (30%), Positives = 158/303 (52%), Gaps = 11/303 (3%) Query: 17 NFLLIVNVLVVLVATWLSRGQFVDIDNLQSMGGQLPELGLLALGIMLSMVSGNGGIDLSG 76 ++++++ L + V + L F+ N++ +G + +G+ A ++ + SG+ DLS Sbjct: 22 DWVMLLAALSIFVLSALFIDNFLSPLNMRGLGLAISTVGIAACTMLFCLASGH--FDLSV 79 Query: 77 VGLANLSGMVAAMLVPRLVNGDDSPVLYTSLFCAIVLMMGLLGGLLNGVVIARLRLTPIL 136 + +G+VA +++ DS VL S L MGL+ GL+NG+VIA+LR+ ++ Sbjct: 80 GSVIACAGVVAGIVI----RDTDSVVLGVSA----ALAMGLVVGLINGIVIAKLRINALI 131 Query: 137 CTLGTQLLFTGFAVVISNGASVHVDYVEPLSDIGNGTVLQVPIAFCIFLAAVIVLGWLLK 196 TL T + G A + SNG +V V E GNG +L VP+ I + + GWLL Sbjct: 132 ATLATMQIVRGLAYIFSNGKAVGV-MDEGFFVFGNGQLLGVPVPIIITVLCFVFFGWLLN 190 Query: 197 RSPFGLRLYLMGTNPKAAFYAGIPRARMLITTYAMCGVLASLAGLISATHTSSAKWDYGN 256 + +G +G N +AA AG+ R I +A+ G++ +LAG+I A+ +S + G Sbjct: 191 YTTYGRNTMAIGGNQEAALLAGVNVDRTKIIIFAVHGLIGALAGVILASRMTSGQPMIGQ 250 Query: 257 SYLLIAILIAVMGGVNPAGGHGRIICVFFAATVLQFLSSLFNLLGVSQFFGDCAWGFLLL 316 + L I V+GGV+ +GG G I V +L + + NL + F+ G +LL Sbjct: 251 GFELTVISACVLGGVSLSGGIGMIRHVIAGVLILAIIENAMNLKNIDTFYQYVIRGSILL 310 Query: 317 LSL 319 L++ Sbjct: 311 LAV 313 Lambda K H 0.327 0.143 0.429 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 333 Number of extensions: 14 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 357 Length of database: 321 Length adjustment: 28 Effective length of query: 329 Effective length of database: 293 Effective search space: 96397 Effective search space used: 96397 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.7 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory